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Old 01-17-2012, 04:13 PM   #1
roshanbernard
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Location: South Korea

Join Date: Feb 2011
Posts: 31
Default annotations intervals problem

Hi guys,

I have two whole genome sequence pf bacteria, mutant and wild type.

I got this annotates in RAST server. and when i try to compare any specific gene and gene product....there is some variation.

for example
In mutant type:
Name: ABC transporter permease protein CDS
Type: CDS
Total Length: 2517 (over 16 intervals)
Interval 16 Length: 501
Interval 16: 1,919,937 -> 1,920,437
Interval 16 Bases: ATCAATCGCGTCAGTCGTAAG...
Intervals: ...1,919,852 -> 1,919,893, 1,919,897 -> 1,919,935, 1,919,937 -> 1,920,437
Bases: GTGAGCAAAATGCGTAAAACA......
NCBI Join Type: join
db_xref: GO:0005215
db_xref: GO:0006810
db_xref: GO:0016020
translation: MSKMRKTILWKDAFQAITHSLGRYIAIILLIGLGTFAFTGLKMAGPDMRATGADFFNKHNLADVTITSNCGINSTDRMTIRNLSEVKKQRLAIFKxx...
product: ABC transporter permease protein
NCBI Feature Key: CDS


In wild type:
Name: ABC transporter permease protein CDS
Type: CDS
Length: 2541
Interval: 1,925,619 -> 1,928,159
Bases: ATGCGTAAAACAATTCTATGG...
db_xref: GO:0005215
db_xref: GO:0006810
db_xref: GO:0016020
translation: MRKTILWKDAFQAITHSLGRYIAIILLIGLGTFAFTGLKMAGPDMRATGADFFNKHNLADVTITSNCGINSTDRMTIRNLSEVKKATFGYFQDVKNK...
product: ABC transporter permease protein
NCBI Feature Key: CDS



can anyone tell me why it shows the gene info as intervals..its happening in many of the CDS....can anyone help me...
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Old 01-18-2012, 05:28 PM   #2
roshanbernard
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Location: South Korea

Join Date: Feb 2011
Posts: 31
Default

Also one more question....

However, However, i have a query about annotation. I have two WGS, one mutant and other wild type.....
while performing the annotation, if there is any mutation in the promoter region, will that be disregarded for annotation??......could u please breif me through it..

i use RAST server for annotation purposes....

could somebody help me...please
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